Identification of circovirus infection in three species of gull

Emergence of novel circoviruses in humans and pigs and their possible importance for xenotransplantation and blood transfusions

BACKGROUND

As sequencing is becoming more broadly available, virus discovery continues. Small DNA viruses contribute to up to 60% of the overall virus load in pigs. Porcine circoviruses (PCVs) are small DNA viruses with a single-stranded circular genome. They are common in pig breeds and have not been properly addressed for their potential risk in xenotransplantation. Whereas PCV1 is non-pathogenic in pigs, PCV2 has been associated with various disease manifestations. Recently two new circoviruses have been described, PCV3 and PCV4. While PCV4 is currently present mainly in Asia, PCV3 is widely distributed, and has been identified in commercial pigs, wild boars, and pigs generated for xenotransplantation. In one case PCV3 was transmitted by pigs to baboons via heart transplantation. PCV3 pathogenicity in pigs was controversial initially, however, the virus was found to be associated with porcine dermatitis and nephropathy syndrome (PDNS), reproductive failure, and multisystemic inflammation. Inoculation studies with PCV3 infectious clones confirmed that PCV3 is pathogenic. Most importantly, recently discovered human circoviruses (CV) are closely related to PCV3.

METHODS

Literature was evaluated and summarized. A dendrogram of existing circoviruses in pigs, humans, and other animal species was created and assessed at the species level.

RESULTS

We found that human circoviruses can be divided into three species, human CV1, CV2, and CV3. Human CV2 and CV3 are closest to PCV3.

CONCLUSIONS

Circoviruses are ubiquitous. This communication should create awareness of PCV3 and the newly discovered human circoviruses, which may be a problem for blood transfusions and xenotransplantation in immune suppressed individuals.

A National Catalogue of Viruses Associated with Indigenous Species Reveals High-Throughput Sequencing as a Driver of Indigenous Virus Discovery

Viruses are important constituents of ecosystems, with the capacity to alter host phenotype and performance. However, virus discovery cued by disease symptoms overlooks latent or beneficial viruses, which are best detected using targeted virus detection or discovered by non-targeted methods, e.g., high-throughput sequencing (HTS). To date, in 64 publications, 701 viruses have been described associated with indigenous species of Aotearoa New Zealand. Viruses were identified in indigenous birds (189 viruses), bats (13 viruses), starfish (4 viruses), insects (280 viruses), and plants (126 viruses). HTS gave rise to a 21.9-fold increase in virus discovery rate over the targeted methods, and 72.7-fold over symptom-based methods. The average number of viruses reported per publication has also increased proportionally over time. The use of HTS has driven the described national virome recently by 549 new-to-science viruses; all are indigenous. This report represents the first catalogue of viruses associated with indigenous species of a country. We provide evidence that the application of HTS to samples of Aotearoa New Zealand's unique fauna and flora has driven indigenous virus discovery, a key step in the process to understand the role of viruses in the biological diversity and ecology of the land, sea, and air environments of a country.

Pigeon Circovirus over Three Decades of Research: Bibliometrics, Scoping Review, and Perspectives

The pigeon circovirus (PiCV), first described in the literature in the early 1990s, is considered one of the most important infectious agents affecting pigeon health. Thirty years after its discovery, the current review has employed bibliometric strategies to map the entire accessible PiCV-related research corpus with the aim of understanding its present research landscape, particularly in consideration of its historical context. Subsequently, developments, current knowledge, and important updates were provided. Additionally, this review also provides a textual analysis examining the relationship between PiCV and the young pigeon disease syndrome (YPDS), as described and propagated in the literature. Our examination revealed that usages of the term 'YPDS' in the literature are characterizations that are diverse in range, and neither standard nor equivalent. Guided by our understanding of the PiCV research corpus, a conceptualization of PiCV diseases was also presented in this review. Proposed definitions and diagnostic criteria for PiCV subclinical infection (PiCV-SI) and PiCV systemic disease (PiCV-SD) were also provided. Lastly, knowledge gaps and open research questions relevant to future PiCV-related studies were identified and discussed.

Establishment of TaqMan-based real-time PCR assay for rapid detection of duck circovirus

Duck circovirus (DuCV) is widespread across the world and causes feather disorders in young ducks. It was identified as the causative pathogen of duck beak atrophy and dwarfism syndrome and primary sclerosing cholangitis. In this study, we aimed to establish a TaqMan-based real-time PCR assay to detect DuCV. The primers and probe were designed based on the conserved region of the DuCV Rep gene. After optimizing the reaction conditions, the minimum virus detection limit of the designed PCR technique was 39.4 copies/μL, 100 times that of conventional PCR (cPCR). No cross-reaction with six other common duck viruses was observed. The intra- and inter-assay variations were less than 1%. The detection rate of DuCV-positive clinical samples using TaqMan-based real-time PCR was higher than that using SYBR Green-based real-time PCR and cPCR. Collectively, these results showed that the established TaqMan-based real-time PCR detected DuCV with high sensitivity and specificity, and significant repeatability, making it suitable for clinical use. Hence, it may be used as a novel tool for the diagnosis and epidemiological investigation of DuCV.

Identification of Circovirus Genome in a Chinstrap Penguin (Pygoscelis antarcticus) and Adélie Penguin (Pygoscelis adeliae) on the Antarctic Peninsula

Circoviruses infect a variety of animal species and have small (~1.8–2.2 kb) circular single-stranded DNA genomes. Recently a penguin circovirus (PenCV) was identified associated with an Adélie Penguin (Pygoscelis adeliae) with feather disorder and in the cloacal swabs of three asymptomatic Adélie Penguins at Cape Crozier, Antarctica. A total of 75 cloacal swab samples obtained from adults and chicks of three species of penguin (genus: Pygoscelis) from seven Antarctic breeding colonies (South Shetland Islands and Western Antarctic Peninsula) in the 2015−2016 breeding season were screened for PenCV. We identified new variants of PenCV in one Adélie Penguin and one Chinstrap Penguin (Pygoscelis antarcticus) from Port Charcot, Booth Island, Western Antarctic Peninsula, a site home to all three species of Pygoscelid penguins. These two PenCV genomes (length of 1986 nucleotides) share > 99% genome-wide nucleotide identity with each other and share ~87% genome-wide nucleotide identity with the PenCV sequences described from Adélie Penguins at Cape Crozier ~4400 km away in East Antarctica. We did not find any evidence of recombination among PenCV sequences. This is the first report of PenCV in Chinstrap Penguins and the first detection outside of Ross Island, East Antarctica. Given the limited knowledge on Antarctic animal viral diversity, future samples from Antarctic wildlife should be screened for these and other viruses to determine the prevalence and potential impact of viral infections.

Seasonal fluctuation of beak and feather disease virus (BFDV) infection in wild Crimson Rosellas (Platycercus elegans)

Understanding patterns of pathogen emergence can help identify mechanisms involved in transmission dynamics. Beak and feather disease virus (BFDV) poses a major threat world-wide to wild and captive parrots. Yet data from wild birds on seasonal fluctuations in prevalence and infection intensity, and thereby the potential high-risk times for virus transmission, have been lacking. We screened wild Crimson Rosellas (Platycercus elegans) for BFDV in blood and cloacal swabs. Prevalence in blood samples and cloacal swabs, as well as viral load varied with Julian date and in blood, were highest after the breeding season. Breeding birds had lower viral load and lower BFDV prevalence in blood than non-breeding birds (10.1% prevalence in breeding vs. 43.2% in non-breeding birds). BFDV prevalence was much higher in younger (<3 years) than older (≥3 years) birds for both blood samples (42.9% vs. 4.5%) and cloacal swabs (56.4% vs. 12.3%). BFDV status in blood and cloacal samples was not correlated within individuals. We show that, at least in P. elegans, BFDV infection seems to occur year-round, with seasonal changes in prevalence and load found in our samples. Our analyses suggest that the seasonal changes were associated primarily with the breeding season. We also discuss age and sex as important predictors of BFDV infection.

GENETIC CHARACTERIZATION OF H13 AND H16 INFLUENZA A VIRUSES IN GULLS (LARUS SPP.) WITH CLINICALLY SEVERE DISEASE AND CONCURRENT CIRCOVIRUS INFECTION

Influenza A viruses (IAVs) of the subtypes H13 and H16 are primarily found in gulls ( Larus spp., order Charadriiformes). Although the gull-adapted subtypes replicate efficiently during infection, gulls usually remain apparently healthy during infection. Avian influenza virus isolates are generally separated into two distinct populations, North American and Eurasian, because of the limited gene flow between the continents. Reassortment between these lineages does occur occasionally; however, direct intercontinental transmission of all eight gene segments is rare. Extensive research has been done to understand the ecology of IAV subtypes that naturally circulate in ducks (order Anseriformes), but the ecology of H13 and H16 IAVs in gulls remains far less studied. In Finland, gulls were screened for IAVs for passive (dead and diseased gulls) and active (clinically healthy gulls) surveillance purposes during the years 2005-10. During that period, 11 H13, two H16 viruses, and one H3N8 IAV were detected. We sequenced partial and full-length hemagglutinin genes of these gull-origin IAVs for phylogenetic assessments. All but one of the H13 genes clustered together with northern European and northeastern Asian viruses, whereas one virus clustered with North American viruses. Interestingly, a high rate (10/14) of these low-pathogenic IAVs was detected in dead or diseased gulls. The atypical clinical status of the IAV-positive gulls and previous observations of circovirus-like inclusion bodies in diseased gulls during autopsies, led us to screen for concurrent circovirus infections in our samples. The DNA of circovirus, an immunosuppressive pathogen of both birds and mammals, was detected in 54% (7/13) of the tested IAV-positive gulls, whereas only 25% (14/56) of our panel of IAV-negative gulls tested positive by circovirus PCR.